Combinatorial analysis of interacting RNA molecules

DOI10.1016/J.MBS.2011.04.009MaRDI QIDQ648014zbMATH OpenOpenAlexWikidataFDO

Authors Thomas J. X. Li, Christian M. Reidys

Publication date 22 November 2011

Published in Mathematical Biosciences (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1006.4089

zbMATH Keywords

joint structureRNA interactionRNA secondary structureshapesingularity analysissymbolic enumeration

Mathematics Subject Classification ID

Symbolic computation and algebraic computation (68W30) Computational methods for problems pertaining to biology (92-08) Biochemistry, molecular biology (92C40)

Abstract: Recently several minimum free energy (MFE) folding algorithms for predicting the joint structure of two interacting RNA molecules have been proposed. Their folding targets are interaction structures, that can be represented as diagrams with two backbones drawn horizontally on top of each other such that (1) intramolecular and intermolecular bonds are noncrossing and (2) there is no "zig-zag" configuration. This paper studies joint structures with arc-length at least four in which both, interior and exterior stack-lengths are at least two (no isolated arcs). The key idea in this paper is to consider a new type of shape, based on which joint structures can be derived via symbolic enumeration. Our results imply simple asymptotic formulas for the number of joint structures with surprisingly small exponential growth rates. They are of interest in the context of designing prediction algorithms for RNA-RNA interactions.

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Cites work

• AN EXAMPLE IN THE THEORY OF THE SPECTRUM OF A FUNCTION
• Combinatorial design of pseudoknot RNA
• Combinatorics of RNA secondary structures
• Combinatorics of RNA-RNA interaction
• scientific article; zbMATH DE number 1268810 (Why is no real title available?)
• Linear trees and RNA secondary structure
• Modular, \(k\)-noncrossing diagrams
• Research in Computational Molecular Biology
• RNA secondary structure: a complete mathematical analysis
• Thermodynamic Analysis of Interacting Nucleic Acid Strands

Cited in

(15)

• A grammatical approach to RNA-RNA interaction prediction
• The block spectrum of RNA pseudoknot structures
• Making multiple RNA interaction practical
• Statistics of topological RNA structures
• Automated prediction of three-way junction topological families in RNA secondary structures
• Using temperature effects to predict the interactions between two RNAs
• Asymptotic number of hairpins of saturated RNA secondary structures
• Gibbs/MCMC sampling for multiple RNA interaction with sub-optimal solutions
• Thermodynamic Analysis of Interacting Nucleic Acid Strands
• Fatgraph models of RNA structure
• Parametric analysis of RNA branching configurations
• Research in Computational Molecular Biology
• NEUTRAL NETWORKS OF INTERACTING RNA SECONDARY STRUCTURES
• Symmetric circular matchings and RNA folding
• Combinatorics of RNA-RNA interaction

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